We have developed a simple and reliable assay to identify small molecule inhibitors of cilia assembly and function. Cilia are sensory and motile organelles that play critical roles in development and disease, including polycystic kidney disease, hydrocephalus, syndromic obesity, chronic sinusitis, bronchiectasis, and retinal degeneration. Small molecule modulators would provide critical tools for studying dynamic events in cilia, and might even point the way to development of pharmacological approaches to ciliary diseases, for which no drugs are currently available. Our assay takes advantage of the model organism Chlamydomonas, which uses cilia to swim to the bottom of an assay well. Because the cells are green, this causes a dark green pellet to self-organize in the well. Mutations or pharmacological treatments which block ciliary motility, or which cause cells to have no cilia, prevent this organization. We have developed image-analysis software that can distinguish these two results in a 96-well format. We have verified the performance of this assay and found it has a Z- value of 0.7 with low plate-to-plate variability and high day-to-day reproducibility. The assay can tolerate DMSO up to 1% and is completely compatible with high throughput robotic methods. We anticipate that a screen using this assay may provide a critical step forward in understanding the mechanisms and treatment of ciliary diseases. Cilia are cellular antennas which project from the surface of most cells in the human body, and sense the surrounding environment. These sensory cilia play critical roles in kidney function, and defects in cilia lead to a devastating disease called polycystic kidney disease. Cilia also play roles in fat metabolism and retina function, and cilia defects can result in genetic obesity and retinal degeneration. Cilia also act like oars to move fluid around cells, and defects in cilia movement can lead to a number of disease symptoms including chronic lung inflammation due to poor mucus clearance, and to hydrocephalus (water on the brain). Currently there are no drugs available to treat diseases, and little is known about how cilia assemble or function. We have developed a new assay for identifying chemical compounds that can affect cilia. These will not only provide important tools for basic research on how cilia work, they would also serve as lead compounds for drug development efforts aimed at treating the large number of ciliary diseases (ciliopathies) that are now known. [unreadable] [unreadable] [unreadable]